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The primary focus of the lab is to understand the genetic basis of variation in complex traits. We exploit multiparent populations (or synthetic populations) and take advantage of genome scale datasets to achieve these goals. We use different genetic model systems depending on the question and approach being used to address a particular problem. We use a diploid outbred population of yeast in an Evolve & Resequence paradigm to understand short-term evolutionary change. The Drosophila Synthetic Population Resource (DSPR) is used to dissect traits in a simple multicellular animal. A fortuitous synthetic population of Peromyscus leucopus is studied to understand how this species is such an effective disease reservoir.

Key Research Areas

yeast robot (youtube link)

Evolve and Resequence in Yeast

We have created an 18-way synthetic population of budding yeast via a diallel cross and further intercrossed the population for 12 generations. This synthetic diploid outbred yeast population can evolved in response to several novel stressors. By virtue of the base population being derived from a set of known founders we can impute founder haplotype frequencies throughout the genome from the poolseq data. We track haplotype (or SNP) frequency changes over time in large samples to ask important questions about how populations respond to a novel environmental challenge. Our system combines many of the advantages of doing evolve and resequence experiments in microbes, except we are working in a system with standing variation and sexual recombination.

image showing DSPR

The DSPR

The Drosophila Synthetic Population Resource (DSPR) consists of a new panel of over 1700 recombinant inbred lines (RILs) of Drosophila melanogaster, derived from two highly recombined synthetic populations, each created by intercrossing a different set of 8 inbred founder lines (with one founder line common to both populations). Complete genome sequence data for the founder lines are available, and in addition, there is a high resolution genetic map for each RIL. The DSPR is widely used by the Drosophila community for high-resolution QTL mapping. We have recently begun exploring a bulked phenotyping and genotyping strategy (X-QTL) which allows us to powerfully map QTL to smaller genetic intervals more easily.

Peromyscus leucopus image

The Genetics of a Disease Reservoir

We are carrying out experiments to identify segregating genetic factors that impact the competence of P. leucopus as a reservoir of B. burgdorferi. A recent genome assembly of P. leucopus in concert with low pass short read sequences from a long-term closed colony can be leveraged to accurately impute SNP and haplotype genotypes on a genome-wide scale. These genotypes are then used to identify genes contributing to the remarkable capacity of P. leucopus to serve as a key reservoir host for B. burgdorferi and other disease agents. The identification of reservoir competence mediating genes may suggest better interventions to block transmission and provide insights into the management of human infections.